Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Abstract

olyploidy or whole-genome duplication provides genomic opportunities for evolutionary innovations in many animal groups and all flowering plants 1-5 , including most important crops such as wheat, cotton and canola or oilseed rape 6-8. The common occurrence of polyploidy may suggest its advantage and potential for selection and adaptation 2,3,9 , through rapid genetic and genomic changes as observed in newly formed Brassica napus 10 , Tragopogon miscellus 11 and polyploid wheat 12 , and/or largely epigenetic modifications as in Arabidopsis and cotton polyploids 5,13. Cotton is a powerful model for revealing genomic insights into polyploidy 3 , providing a phylogenetically defined framework of polyploidization (~1.5 million years ago (Ma)) 14 , followed by natural diversification and crop domestication 15. The evolutionary history of the polyploid cotton clade is longer than that of some other allopolyploids, such as hexaploid wheat (~8,000 years) 12 , tetraploid canola (~7,500 years) 16 and tetraploid Tragopogon (~150 years) 11. Polyploidization between an A-genome African species (Gossypium arboreum (Ga)-like) and a D-genome American species (G. raimondii (Gr)-like) in the New World created a new allotetraploid or amphidiploid (AD-genome) cotton clade (Fig. 1a) 14 , which has diversified into five polyploid lineages, G. hirsutum (Gh) (AD) 1 , G. barbadense (Gb) (AD) 2 , G. tomentosum (Gt) (AD) 3 , G. mustelinum (Gm) (AD) 4 and G. darwinii (Gd) (AD) 5. G. ekmanianum and G. stephensii are recently characterized and closely related to Gh 17. Gh and Gb were separately domesticated from perennial shrubs to become annualized Upland and Pima cottons 15. To date, global cotton production provides income for ~100 million families across ~150 countries, with an annual economic impact of ~US$500 billion worldwide 6. However, cotton supply is reduced due to aridification, climate change and pest emergence. Future improvements in cotton and sustainability will involve use of the genomic resources and gene-editing tools becoming available in many crops 9,18,19. Cotton genomes have been sequenced for the D-genome (Gr) 20 and A-genome (Ga) 21 diploids and two cultivated tetraploids 22-26. These analyses have shown structural, genetic and gene expression variation related to fiber traits and stress responses in cultivated

Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding

“…In view of cotton's importance in human life, intensive efforts have been focused on uncovering the genome mysteries of cotton species. Three diploid cottons and two tetraploid cottons were sequenced, including G. arboreum (Li et al, 2014;Du et al, 2018;Huang et al, 2020), G. herbaceum (Huang et al, 2020), G. raimondii (Wang et al, 2012;Paterson et al, 2012;Udall et al, 2019), G. hirsutum (Li et al, 2015;Zhang et al, 2015;Hu et al, 2019;Wang M. et al, 2019;Chen et al, 2020;Huang et al, 2020) and G. barbadense (Yuan et al, 2015;Liu et al, 2015;Hu et al, 2019;Wang M. et al, 2019;Chen et al, 2020). Detailed genome information is shown in Tables 1 and 2.…”

“…G. arboretum (Li et al, 2014) G. arboretum (Du et al, 2018) G. arboretum (Huang et al, 2020) G. herbaceum (Huang et al, 2020) G. raimondii (Wang et al, 2012) G. raimondii (Paterson et al, 2012) G. raimondii (Udall et al, 2019) Total contigs 40,381 8,223 2,432 1,781 41,307 19,735 187 Contig N50 (kb) 72 1,100 1, G. hirsutum (TM-1,V1.1) (Zhang et al, 2015) G. hirsutum (TM-1) (Wang M. et al, 2019) G. hirsutum (TM-1,V2.1) (Hu et al, 2019) G. hirsutum (TM-1,updated V1) (Huang et al, 2020) G. hirsutum (TM-1) (Chen et al, 2020) G. barbadense (Xinhai21) (Liu et al, 2015) G. barbadense…”

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

“…Genes involved in phytohormone signaling and biosynthesis are crucial for the transition from NEC to EC. In total, there are 6,132 genes annotated as a phytohormone in the Gossypium hirsutum (CV TM1) reference genome assembly [49]. In general, we observed an abundance of phytohormone related genes being downregulated in EC callus relative to NEC (Table 3).…”

“…Preprocessed reads were aligned to the Gossypium hirsutum v2.0 reference assembly (Chen et al, 2020) with the Bowtie2 short read aligner [93], and alignment les were coordinate sorted and indexed with samtools v1.3.1 [94]. Raw counts, FPKM and TMM values were generated with RSEM [95].…”

Version 4.3-12/08/20 Cotton bZIP Transcription Factors: Characterization of the bZIP Family From Gossypium Hirsutum, Gossypium Arboreum and Gossypium Raimondii

“…Cultivated G. arboreum, A subgenome species, and its counterpart, non-spinnable ber producer G. raimondii, D subgenome species are two progenitor species of cultivated allotetraploid cotton, G.hirsutum (Li et al 2014). Estimated genome size of G. hirsutum is ~2305.2Mb (Chen et al 2020). Estimated genome size of G. arboreum is ~1746Mb which is around two fold larger than G. raimondii, ~880Mb (Hendrix et al 2005).…”